Balancing up and downregulation of the C. elegans X chromosomes

Lau, Alyssa C.; Csankovszki, Györgyi

doi:10.1016/j.gde.2015.04.001

Cited by 29 publications

(36 citation statements)

References 57 publications

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“…The EE and L3 autosomal chromatin states show much greater similarity to each other than do the EE and L3 chromosome X states (Figs. S1 and S2), consistent with alterations in chromatin structure and marking induced by dosage compensation after the EE stage (16). The chromatin states were annotated by analyzing the associations of states with a range of different genomic features ( Fig.…”

Section: Resultsmentioning

confidence: 82%

“…We found that inactive and lowly expressed genes are associated with states [16][17][18][19][20] (Fig. S1).…”

Section: Resultsmentioning

confidence: 86%

“…To investigate features and domain organization of C. elegans chromatin, we derived 20 state EE and L3 chromatin state maps, using hidden Markov models (HMM) and ChIP data for 17 histones or modifications (Materials and Methods). Patterns and levels of enrichment of many histone modifications differ on C. elegans autosomes compared with the X chromosome, reflecting dosage compensation (7,(16)(17)(18), which caused whole-genome chromatin state maps to subdivide into separate autosomal and X-chromosome-specific states. Therefore, for each stage we generated a separate map for autosomes and the X chromosome (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Actively transcribed genes reside on the chromosome arms and these genes are marked by histone modifications associated with gene activity, as in the central regions (7). In addition, the X chromosome shows extensive chromatin differences compared with autosomes because of dosage compensation (16). These previous studies have provided a large-scale picture of C. elegans chromosome organization.…”

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confidence: 97%

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Stable Caenorhabditis elegans chromatin domains separate broadly expressed and developmentally regulated genes

Evans

Huang

Stempor

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

148

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Eukaryotic genomes are organized into domains of differing structure and activity. There is evidence that the domain organization of the genome regulates its activity, yet our understanding of domain properties and the factors that influence their formation is poor. Here, we use chromatin state analyses in early embryos and third-larval stage (L3) animals to investigate genome domain organization and its regulation in Caenorhabditis elegans. At both stages we find that the genome is organized into extended chromatin domains of high or low gene activity defined by different subsets of states, and enriched for H3K36me3 or H3K27me3, respectively. The border regions between domains contain large intergenic regions and a high density of transcription factor binding, suggesting a role for transcription regulation in separating chromatin domains. Despite the differences in cell types, overall domain organization is remarkably similar in early embryos and L3 larvae, with conservation of 85% of domain border positions. Most genes in highactivity domains are expressed in the germ line and broadly across cell types, whereas low-activity domains are enriched for genes that are developmentally regulated. We find that domains are regulated by the germ-line H3K36 methyltransferase MES-4 and that border regions show striking remodeling of H3K27me1, supporting roles for H3K36 and H3K27 methylation in regulating domain structure. Our analyses of C. elegans chromatin domain structure show that genes are organized by type into domains that have differing modes of regulation.chromatin states | chromatin domains | C. elegans | boundary

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Section: Resultsmentioning

confidence: 82%

“…We found that inactive and lowly expressed genes are associated with states [16][17][18][19][20] (Fig. S1).…”

Section: Resultsmentioning

confidence: 86%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 97%

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Stable Caenorhabditis elegans chromatin domains separate broadly expressed and developmentally regulated genes

Evans

Huang

Stempor

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

148

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“…This is in contrast to dosage compensation in mammals where in cells carrying two X chromosomes, one of the X chromosomes is inactivated while dosage-sensitive genes in the other are upregulated (Deng et al 2011). A key component of the dosage-compensation machinery in C. elegans is the dosage compensation complex (DCC), which is structurally similar to the condensin complex that can induce structural changes to DNA (Sharma et al 2014;Lau and Csankovszki 2015). Both FISH and Hi-C data suggest that the DCC leads to compaction of chromosome X in XX animals.…”

Section: Features Of C Elegans Chromosome Organizationmentioning

confidence: 98%

Cell Biology of theCaenorhabditis elegansNucleus

Cohen-Fix

Askjaer

2017

Genetics

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Studies on the Caenorhabditis elegans nucleus have provided fascinating insight to the organization and activities of eukaryotic cells. Being the organelle that holds the genetic blueprint of the cell, the nucleus is critical for basically every aspect of cell biology. The stereotypical development of C. elegans from a one cell-stage embryo to a fertile hermaphrodite with 959 somatic nuclei has allowed the identification of mutants with specific alterations in gene expression programs, nuclear morphology, or nuclear positioning. Moreover, the early C. elegans embryo is an excellent model to dissect the mitotic processes of nuclear disassembly and reformation with high spatiotemporal resolution. We review here several features of the C. elegans nucleus, including its composition, structure, and dynamics. We also discuss the spatial organization of chromatin and regulation of gene expression and how this depends on tight control of nucleocytoplasmic transport. Finally, the extensive connections of the nucleus with the cytoskeleton and their implications during development are described. Most processes of the C. elegans nucleus are evolutionarily conserved, highlighting the relevance of this powerful and versatile model organism to human biology.KEYWORDS Caenorhabditis elegans; chromatin; gene expression; lamin; LEM-domain proteins; LINC; P granule; nuclear pore complex; nuclear envelope; nucleocytoplasmic transport; nucleolus; WormBook TABLE OF CONTENTSAbstract 25 C. elegans as a model system to study cell biology of the nucleus 26 Structural components of the nucleus 27

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Condensin action and compaction

2018

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Condensin is a multi-subunit protein complex that belongs to the family of structural maintenance of chromosomes (SMC) complexes. Condensins regulate chromosome structure in a wide range of processes including chromosome segregation, gene regulation, DNA repair and recombination.Recent research defined the structural features and molecular activities of condensins, but it is unclear how these activities are connected to the multitude of phenotypes and functions attributed to condensins. In this review, we briefly discuss the different molecular mechanisms by which condensins may regulate global chromosome compaction, organization of topologically associated domains, clustering of specific loci such as tRNA genes, rDNA segregation, and gene regulation.

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Balancing up and downregulation of the C. elegans X chromosomes

Cited by 29 publications

References 57 publications

Stable Caenorhabditis elegans chromatin domains separate broadly expressed and developmentally regulated genes

Stable Caenorhabditis elegans chromatin domains separate broadly expressed and developmentally regulated genes

Cell Biology of theCaenorhabditis elegansNucleus

Condensin action and compaction

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